Role of Lys-226 in the Catalytic Mechanism ofBacillus StearothermophilusSerine HydroxymethyltransferaseCrystal Structure and Kinetic Studies†,‡

Biochemistry ◽  
2005 ◽  
Vol 44 (18) ◽  
pp. 6929-6937 ◽  
Author(s):  
Siddegowda Bhavani ◽  
V. Trivedi ◽  
V. R. Jala ◽  
H. S. Subramanya ◽  
Purnima Kaul ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Kinetic Studies

Multifunctional Role of Tyr 108 in the Catalytic Mechanism of Human Glutathione Transferase P1-1. Crystallographic and Kinetic Studies on the Y108F Mutant Enzyme†,‡

Biochemistry ◽  
1997 ◽  
Vol 36 (20) ◽  
pp. 6207-6217 ◽  
Author(s):  
Mario Lo Bello ◽  
Aaron J. Oakley ◽  
Andrea Battistoni ◽  
Anna P. Mazzetti ◽  
Marzia Nuccetelli ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Glutathione Transferase ◽  
Kinetic Studies ◽  
Mutant Enzyme

Study of the catalytic mechanism of a non-heme Fe catalyst: The role of the spin state of the iron

2021 ◽  
Vol 764 ◽  
pp. 138282
Author(s):  
Aikaterini Gemenetzi ◽  
Panagiota Stathi ◽  
Yiannis Deligiannakis ◽  
Maria Louloudi
Keyword(s):  
Spin State ◽  
Catalytic Mechanism ◽  
Fe Catalyst

Probing the Role of Tyr 64 ofTreponema denticolaCystalysin by Site-Directed Mutagenesis and Kinetic Studies†

Biochemistry ◽  
2005 ◽  
Vol 44 (42) ◽  
pp. 13970-13980 ◽  
Author(s):  
Barbara Cellini ◽  
Mariarita Bertoldi ◽  
Riccardo Montioli ◽  
Carla Borri Voltattorni
Keyword(s):  
Kinetic Studies ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis

Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism

2001 ◽  
Vol 359 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Valeria MENCHISE ◽  
Catherine CORBIER ◽  
Claude DIDIERJEAN ◽  
Michele SAVIANO ◽  
Ettore BENEDETTI ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Proton Transfer ◽  
Chlamydomonas Reinhardtii ◽  
Catalytic Mechanism ◽  
Structural Data ◽  
Careful Analysis ◽  
Wild Type ◽  
Thioredoxin H ◽  
Dynamics Simulations

Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.

Structure−Function Relationships in Human Glutathione-Dependent Formaldehyde Dehydrogenase. Role of Glu-67 and Arg-368 in the Catalytic Mechanism†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (15) ◽  
pp. 4819-4830 ◽  
Author(s):  
Paresh C. Sanghani ◽  
Wilhelmina I. Davis ◽  
LanMin Zhai ◽  
Howard Robinson
Keyword(s):  
Structure Function ◽  
Catalytic Mechanism ◽  
Formaldehyde Dehydrogenase

The Role of Reducible Oxide–Metal Cluster Charge Transfer in Catalytic Processes: New Insights on the Catalytic Mechanism of CO Oxidation on Au/TiO2 from ab Initio Molecular Dynamics

2013 ◽  
Vol 135 (29) ◽  
pp. 10673-10683 ◽  
Author(s):  
Yang-Gang Wang ◽  
Yeohoon Yoon ◽  
Vassiliki-Alexandra Glezakou ◽  
Jun Li ◽  
Roger Rousseau
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Ab Initio ◽  
Co Oxidation ◽  
Catalytic Mechanism ◽  
Metal Cluster ◽  
Ab Initio Molecular Dynamics ◽  
Catalytic Processes

Crystallographic and Enzymic Investigations on the Role of Ser558, His610, and Asn614 in the Catalytic Mechanism of Azotobacter vinelandii Dihydrolipoamide Acetyltransferase (E2p)

Biochemistry ◽  
1995 ◽  
Vol 34 (13) ◽  
pp. 4287-4298 ◽  
Author(s):  
Joerg Hendle ◽  
Andrea Mattevi ◽  
Adrie H. Westphal ◽  
Johan Spee ◽  
Arie de Kok ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Azotobacter Vinelandii

scholarly journals On the Role of Pre- and Post-Electron-Transfer Steps in the SmI2/Amine/H2O-Mediated Reduction of Esters: New Mechanistic Insights and Kinetic Studies

2014 ◽  
Vol 20 (15) ◽  
pp. 4222-4226 ◽  
Author(s):  
Michal Szostak ◽  
Malcolm Spain ◽  
David J. Procter
Keyword(s):  
Electron Transfer ◽  
Kinetic Studies ◽  
Mediated Reduction

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

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